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<title>Computer Assited Medical Intervention Tool Kit: Atom Class Reference</title>
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<div id="projectname">Computer Assited Medical Intervention Tool Kit
 <span id="projectnumber">version 4.0</span>
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<a href="#pub-methods">Public Member Functions</a> |
<a href="#pri-attribs">Private Attributes</a> |
<a href="classAtom-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">Atom Class Reference<div class="ingroups"><a class="el" href="group__group__cepmodeling.html">CEP Modeling</a> » <a class="el" href="group__group__cepmodeling__libraries.html">Libraries</a> » <a class="el" href="group__group__cepmodeling__libraries__pml.html">PML</a></div></div> </div>
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<p>An atom has an unique index in the physical model object, a 3D position, and different basic properties.
<a href="classAtom.html#details">More...</a></p>
<p><code>#include <<a class="el" href="Atom_8h_source.html">Atom.h</a>></code></p>
<p>Inherits <a class="el" href="classStructure.html">Structure</a>.</p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a86406a7587112d736dbdc9170ec23b2c"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#a86406a7587112d736dbdc9170ec23b2c">Atom</a> (<a class="el" href="classPhysicalModel.html">PhysicalModel</a> *myPM)</td></tr>
<tr class="memdesc:a86406a7587112d736dbdc9170ec23b2c"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor : set the position to the origin, generate a unique index. <a href="#a86406a7587112d736dbdc9170ec23b2c">More...</a><br /></td></tr>
<tr class="separator:a86406a7587112d736dbdc9170ec23b2c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a28755c30bfc63e44babeaa264025c2b9"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#a28755c30bfc63e44babeaa264025c2b9">Atom</a> (<a class="el" href="classPhysicalModel.html">PhysicalModel</a> *myPM, physicalModel::Atom atom, unsigned int id=-1)</td></tr>
<tr class="memdesc:a28755c30bfc63e44babeaa264025c2b9"><td class="mdescLeft"> </td><td class="mdescRight">constructor from xml node: try to read and get the parameters from xml and set the index in atom SC (if possible) <a href="#a28755c30bfc63e44babeaa264025c2b9">More...</a><br /></td></tr>
<tr class="separator:a28755c30bfc63e44babeaa264025c2b9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a94983b269cc598424e97b30895c88bda"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#a94983b269cc598424e97b30895c88bda">Atom</a> (<a class="el" href="classPhysicalModel.html">PhysicalModel</a> *myPM, const double pos[3])</td></tr>
<tr class="memdesc:a94983b269cc598424e97b30895c88bda"><td class="mdescLeft"> </td><td class="mdescRight">constructor : generate a unique index <a href="#a94983b269cc598424e97b30895c88bda">More...</a><br /></td></tr>
<tr class="separator:a94983b269cc598424e97b30895c88bda"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a32e11d4ca59dffa3d58654ead0108f31"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#a32e11d4ca59dffa3d58654ead0108f31">Atom</a> (<a class="el" href="classPhysicalModel.html">PhysicalModel</a> *myPM, const unsigned int ind)</td></tr>
<tr class="memdesc:a32e11d4ca59dffa3d58654ead0108f31"><td class="mdescLeft"> </td><td class="mdescRight">set the position to the origin <a href="#a32e11d4ca59dffa3d58654ead0108f31">More...</a><br /></td></tr>
<tr class="separator:a32e11d4ca59dffa3d58654ead0108f31"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a66553665577ec68ec9bbdd57621c6154"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#a66553665577ec68ec9bbdd57621c6154">Atom</a> (<a class="el" href="classPhysicalModel.html">PhysicalModel</a> *myPM, const unsigned int ind, const double pos[3])</td></tr>
<tr class="memdesc:a66553665577ec68ec9bbdd57621c6154"><td class="mdescLeft"> </td><td class="mdescRight">constructor : generate a unique index <a href="#a66553665577ec68ec9bbdd57621c6154">More...</a><br /></td></tr>
<tr class="separator:a66553665577ec68ec9bbdd57621c6154"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8408c7d4ed28ab1c0ef49035ccea4e86"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#a8408c7d4ed28ab1c0ef49035ccea4e86">getIndexInAtoms</a> () const</td></tr>
<tr class="memdesc:a8408c7d4ed28ab1c0ef49035ccea4e86"><td class="mdescLeft"> </td><td class="mdescRight">get the index of this atom in the global atom structural component, i.e. its order number in atoms <a href="#a8408c7d4ed28ab1c0ef49035ccea4e86">More...</a><br /></td></tr>
<tr class="separator:a8408c7d4ed28ab1c0ef49035ccea4e86"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4ac7762cfcdfff37fe8cd4370a24d79b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#a4ac7762cfcdfff37fe8cd4370a24d79b">getPosition</a> (double pos[3]) const</td></tr>
<tr class="memdesc:a4ac7762cfcdfff37fe8cd4370a24d79b"><td class="mdescLeft"> </td><td class="mdescRight">get the position of the atom (array of 3 doubles) <a href="#a4ac7762cfcdfff37fe8cd4370a24d79b">More...</a><br /></td></tr>
<tr class="separator:a4ac7762cfcdfff37fe8cd4370a24d79b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acb191b6088ce3d936909d9f7c5fc8848"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classAtomProperties.html">AtomProperties</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#acb191b6088ce3d936909d9f7c5fc8848">getProperties</a> () const</td></tr>
<tr class="memdesc:acb191b6088ce3d936909d9f7c5fc8848"><td class="mdescLeft"> </td><td class="mdescRight">Get a ptr to the <a class="el" href="classAtomProperties.html" title="This class manages all the properties attached to an atom. ">AtomProperties</a>. <a href="#acb191b6088ce3d936909d9f7c5fc8848">More...</a><br /></td></tr>
<tr class="separator:acb191b6088ce3d936909d9f7c5fc8848"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae658592f948de366f4946af0c87370c3"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#ae658592f948de366f4946af0c87370c3">isInstanceOf</a> (const char *) const</td></tr>
<tr class="memdesc:ae658592f948de366f4946af0c87370c3"><td class="mdescLeft"> </td><td class="mdescRight">return true only if the parameter is equal to "Atom" <a href="#ae658592f948de366f4946af0c87370c3">More...</a><br /></td></tr>
<tr class="separator:ae658592f948de366f4946af0c87370c3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aab8d61ef48ffe599b893391dd845db6d"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#aab8d61ef48ffe599b893391dd845db6d">setIndex</a> (const unsigned int)</td></tr>
<tr class="memdesc:aab8d61ef48ffe599b893391dd845db6d"><td class="mdescLeft"> </td><td class="mdescRight">set the index. <a href="#aab8d61ef48ffe599b893391dd845db6d">More...</a><br /></td></tr>
<tr class="separator:aab8d61ef48ffe599b893391dd845db6d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a873c3f281c5ae9b52ccf33a64624edc0"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#a873c3f281c5ae9b52ccf33a64624edc0">setPosition</a> (const double [3])</td></tr>
<tr class="memdesc:a873c3f281c5ae9b52ccf33a64624edc0"><td class="mdescLeft"> </td><td class="mdescRight">set the position of the atom <a href="#a873c3f281c5ae9b52ccf33a64624edc0">More...</a><br /></td></tr>
<tr class="separator:a873c3f281c5ae9b52ccf33a64624edc0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a47aa4312038dac24da76fde7eec8ba5f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#a47aa4312038dac24da76fde7eec8ba5f">setPosition</a> (const double, const double, const double)</td></tr>
<tr class="memdesc:a47aa4312038dac24da76fde7eec8ba5f"><td class="mdescLeft"> </td><td class="mdescRight">set the position of the atom <a href="#a47aa4312038dac24da76fde7eec8ba5f">More...</a><br /></td></tr>
<tr class="separator:a47aa4312038dac24da76fde7eec8ba5f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0a6980eff6c5753e153b97b75bb831dc"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#a0a6980eff6c5753e153b97b75bb831dc">xmlPrint</a> (std::ostream &, const <a class="el" href="classStructuralComponent.html">StructuralComponent</a> *)</td></tr>
<tr class="memdesc:a0a6980eff6c5753e153b97b75bb831dc"><td class="mdescLeft"> </td><td class="mdescRight">print to an output stream in "pseudo" XML format. <a href="#a0a6980eff6c5753e153b97b75bb831dc">More...</a><br /></td></tr>
<tr class="separator:a0a6980eff6c5753e153b97b75bb831dc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6926cfb6d5e61ca21c71476b66547a5e"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#a6926cfb6d5e61ca21c71476b66547a5e">~Atom</a> ()</td></tr>
<tr class="memdesc:a6926cfb6d5e61ca21c71476b66547a5e"><td class="mdescLeft"> </td><td class="mdescRight">std destructor <a href="#a6926cfb6d5e61ca21c71476b66547a5e">More...</a><br /></td></tr>
<tr class="separator:a6926cfb6d5e61ca21c71476b66547a5e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classStructure"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classStructure')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classStructure.html">Structure</a></td></tr>
<tr class="memitem:aee69ddf2513ad465e91281c91597f42e inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#aee69ddf2513ad465e91281c91597f42e">addStructuralComponent</a> (<a class="el" href="classStructuralComponent.html">StructuralComponent</a> *)</td></tr>
<tr class="memdesc:aee69ddf2513ad465e91281c91597f42e inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">add a particular <a class="el" href="classStructuralComponent.html" title="A structural component is composed either by cell or by atoms. ">StructuralComponent</a> in the list <a href="classStructure.html#aee69ddf2513ad465e91281c91597f42e">More...</a><br /></td></tr>
<tr class="separator:aee69ddf2513ad465e91281c91597f42e inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9a21135d09e8292affb68647dee9d1a7 inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classStructuralComponent.html">StructuralComponent</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#a9a21135d09e8292affb68647dee9d1a7">getAllStructuralComponents</a> ()</td></tr>
<tr class="memdesc:a9a21135d09e8292affb68647dee9d1a7 inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">get the list of all the <a class="el" href="classStructuralComponent.html" title="A structural component is composed either by cell or by atoms. ">StructuralComponent</a> that are using this structure <a href="classStructure.html#a9a21135d09e8292affb68647dee9d1a7">More...</a><br /></td></tr>
<tr class="separator:a9a21135d09e8292affb68647dee9d1a7 inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a04b2fc52d7cc2af4356620f1d7e09c18 inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#a04b2fc52d7cc2af4356620f1d7e09c18">getIndex</a> () const</td></tr>
<tr class="memdesc:a04b2fc52d7cc2af4356620f1d7e09c18 inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">get the structure unique index (stored in its property) <a href="classStructure.html#a04b2fc52d7cc2af4356620f1d7e09c18">More...</a><br /></td></tr>
<tr class="separator:a04b2fc52d7cc2af4356620f1d7e09c18 inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a169a753f6b51f193cb5d62294b4b02be inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#a169a753f6b51f193cb5d62294b4b02be">getName</a> () const</td></tr>
<tr class="memdesc:a169a753f6b51f193cb5d62294b4b02be inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">get the name of the structure <a href="classStructure.html#a169a753f6b51f193cb5d62294b4b02be">More...</a><br /></td></tr>
<tr class="separator:a169a753f6b51f193cb5d62294b4b02be inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a58d9d946f94837c5a2141d3c7f250adf inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#a58d9d946f94837c5a2141d3c7f250adf">getNumberOfStructuralComponents</a> () const</td></tr>
<tr class="memdesc:a58d9d946f94837c5a2141d3c7f250adf inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">get the number of <a class="el" href="classStructuralComponent.html" title="A structural component is composed either by cell or by atoms. ">StructuralComponent</a> that are using this structure <a href="classStructure.html#a58d9d946f94837c5a2141d3c7f250adf">More...</a><br /></td></tr>
<tr class="separator:a58d9d946f94837c5a2141d3c7f250adf inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae259369164469377b42ba25912439338 inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classStructuralComponent.html">StructuralComponent</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#ae259369164469377b42ba25912439338">getStructuralComponent</a> (unsigned int i)</td></tr>
<tr class="memdesc:ae259369164469377b42ba25912439338 inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">get a particular <a class="el" href="classStructuralComponent.html" title="A structural component is composed either by cell or by atoms. ">StructuralComponent</a> that is using this structure <a href="classStructure.html#ae259369164469377b42ba25912439338">More...</a><br /></td></tr>
<tr class="separator:ae259369164469377b42ba25912439338 inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8fd619e1b2635bd473bf182d0528f9c7 inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classStructureProperties.html#a9180a07ccc47844f526e879201d75731">StructureProperties::GeometricType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#a8fd619e1b2635bd473bf182d0528f9c7">getType</a> () const</td></tr>
<tr class="memdesc:a8fd619e1b2635bd473bf182d0528f9c7 inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">get the type of index <a href="classStructure.html#a8fd619e1b2635bd473bf182d0528f9c7">More...</a><br /></td></tr>
<tr class="separator:a8fd619e1b2635bd473bf182d0528f9c7 inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0eb7c50fc8aff59e51ec6c895a79601b inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#a0eb7c50fc8aff59e51ec6c895a79601b">removeStructuralComponent</a> (<a class="el" href="classStructuralComponent.html">StructuralComponent</a> *)</td></tr>
<tr class="memdesc:a0eb7c50fc8aff59e51ec6c895a79601b inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">remove a particular <a class="el" href="classStructuralComponent.html" title="A structural component is composed either by cell or by atoms. ">StructuralComponent</a> from the list <a href="classStructure.html#a0eb7c50fc8aff59e51ec6c895a79601b">More...</a><br /></td></tr>
<tr class="separator:a0eb7c50fc8aff59e51ec6c895a79601b inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aca4dbb99fb713e922fbb33397343ccb0 inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#aca4dbb99fb713e922fbb33397343ccb0">setName</a> (std::string)</td></tr>
<tr class="memdesc:aca4dbb99fb713e922fbb33397343ccb0 inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">set the name of the structure <a href="classStructure.html#aca4dbb99fb713e922fbb33397343ccb0">More...</a><br /></td></tr>
<tr class="separator:aca4dbb99fb713e922fbb33397343ccb0 inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa53e0a158a491c782c858436896b9c02 inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#aa53e0a158a491c782c858436896b9c02">setPhysicalModel</a> (<a class="el" href="classPhysicalModel.html">PhysicalModel</a> *)</td></tr>
<tr class="memdesc:aa53e0a158a491c782c858436896b9c02 inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">set the physical model <a href="classStructure.html#aa53e0a158a491c782c858436896b9c02">More...</a><br /></td></tr>
<tr class="separator:aa53e0a158a491c782c858436896b9c02 inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac6c101b28efea5a150cce3bb8948f8d1 inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#ac6c101b28efea5a150cce3bb8948f8d1">Structure</a> ()</td></tr>
<tr class="memdesc:ac6c101b28efea5a150cce3bb8948f8d1 inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">Base constructor. <a href="classStructure.html#ac6c101b28efea5a150cce3bb8948f8d1">More...</a><br /></td></tr>
<tr class="separator:ac6c101b28efea5a150cce3bb8948f8d1 inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9b0688285fa394f7b93b1b4edd6a5fbf inherit pub_methods_classStructure"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#a9b0688285fa394f7b93b1b4edd6a5fbf">~Structure</a> ()</td></tr>
<tr class="memdesc:a9b0688285fa394f7b93b1b4edd6a5fbf inherit pub_methods_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor needed here as this is an abstract class (pure virtual) <a href="classStructure.html#a9b0688285fa394f7b93b1b4edd6a5fbf">More...</a><br /></td></tr>
<tr class="separator:a9b0688285fa394f7b93b1b4edd6a5fbf inherit pub_methods_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
Private Attributes</h2></td></tr>
<tr class="memitem:aba7e868fb492a66507780d8c9f4af6e7"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="classAtom.html#aba7e868fb492a66507780d8c9f4af6e7">indexInAtoms</a></td></tr>
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Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_attribs_classStructure"><td colspan="2" onclick="javascript:toggleInherit('pub_attribs_classStructure')"><img src="closed.png" alt="-"/> Public Attributes inherited from <a class="el" href="classStructure.html">Structure</a></td></tr>
<tr class="memitem:a711e022b372da3d0bdfd5ea5bb34c91b inherit pub_attribs_classStructure"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#a711e022b372da3d0bdfd5ea5bb34c91b">hasIndex</a></td></tr>
<tr class="memdesc:a711e022b372da3d0bdfd5ea5bb34c91b inherit pub_attribs_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">indicate if the <a class="el" href="classStructure.html" title="Pure virtual class that represent an element of the structure. ">Structure</a> has an index (which is not the case all the time) <a href="classStructure.html#a711e022b372da3d0bdfd5ea5bb34c91b">More...</a><br /></td></tr>
<tr class="separator:a711e022b372da3d0bdfd5ea5bb34c91b inherit pub_attribs_classStructure"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_attribs_classStructure"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classStructure')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classStructure.html">Structure</a></td></tr>
<tr class="memitem:a693e6b047fc6bb216b7646e0c2599070 inherit pro_attribs_classStructure"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classStructureProperties.html">StructureProperties</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classStructure.html#a693e6b047fc6bb216b7646e0c2599070">properties</a></td></tr>
<tr class="memdesc:a693e6b047fc6bb216b7646e0c2599070 inherit pro_attribs_classStructure"><td class="mdescLeft"> </td><td class="mdescRight">Property of the current structure. <a href="classStructure.html#a693e6b047fc6bb216b7646e0c2599070">More...</a><br /></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>An atom has an unique index in the physical model object, a 3D position, and different basic properties. </p>
<p>It is the most basic structure composing a physical model. It is on an atoms that the forces and loads could be applied in order to generate dynamics. </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a86406a7587112d736dbdc9170ec23b2c">◆ </a></span>Atom() <span class="overload">[1/5]</span></h2>
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<td class="memname">Atom::Atom </td>
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<p>Default constructor : set the position to the origin, generate a unique index. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">myPM</td><td>the physical model the atom belongs to </td></tr>
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</dd>
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<p class="reference">References <a class="el" href="classStructure.html#a693e6b047fc6bb216b7646e0c2599070">Structure::properties</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a28755c30bfc63e44babeaa264025c2b9">◆ </a></span>Atom() <span class="overload">[2/5]</span></h2>
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<td class="memname">Atom::Atom </td>
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<td class="paramtype"><a class="el" href="classPhysicalModel.html">PhysicalModel</a> * </td>
<td class="paramname"><em>myPM</em>, </td>
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<td class="paramtype">physicalModel::Atom </td>
<td class="paramname"><em>atom</em>, </td>
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<td class="paramtype">unsigned int </td>
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<p>constructor from xml node: try to read and get the parameters from xml and set the index in atom SC (if possible) </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">myPM</td><td>the physical model the atom belongs to </td></tr>
<tr><td class="paramname">atom</td><td>the xsd class representing the atom to read information from. </td></tr>
<tr><td class="paramname">id</td><td>the index in the atoms structural component (useful to directly access the memory block corresponding to the position) </td></tr>
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</dd>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="classAtom.html#a8408c7d4ed28ab1c0ef49035ccea4e86" title="get the index of this atom in the global atom structural component, i.e. its order number in atoms ...">getIndexInAtoms()</a> </dd></dl>
<p class="reference">References <a class="el" href="classAtom.html#aba7e868fb492a66507780d8c9f4af6e7">indexInAtoms</a>, and <a class="el" href="classStructure.html#a693e6b047fc6bb216b7646e0c2599070">Structure::properties</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a94983b269cc598424e97b30895c88bda">◆ </a></span>Atom() <span class="overload">[3/5]</span></h2>
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<td class="memname">Atom::Atom </td>
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<td class="paramtype">const double </td>
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<p>constructor : generate a unique index </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">myPM</td><td>the physical model the atom belongs to </td></tr>
<tr><td class="paramname">pos</td><td>the initial position of the created atom (array of 3 double) </td></tr>
</table>
</dd>
</dl>
<p class="reference">References <a class="el" href="classStructure.html#a693e6b047fc6bb216b7646e0c2599070">Structure::properties</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a32e11d4ca59dffa3d58654ead0108f31">◆ </a></span>Atom() <span class="overload">[4/5]</span></h2>
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<td class="memname">Atom::Atom </td>
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<td class="paramtype"><a class="el" href="classPhysicalModel.html">PhysicalModel</a> * </td>
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<td class="paramtype">const unsigned int </td>
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<p>set the position to the origin </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">myPM</td><td>the physical model the atom belongs to </td></tr>
<tr><td class="paramname">ind</td><td>give the unique index </td></tr>
</table>
</dd>
</dl>
<p class="reference">References <a class="el" href="classStructure.html#a693e6b047fc6bb216b7646e0c2599070">Structure::properties</a>.</p>
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<td class="memname">Atom::Atom </td>
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<td class="paramtype"><a class="el" href="classPhysicalModel.html">PhysicalModel</a> * </td>
<td class="paramname"><em>myPM</em>, </td>
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<td class="paramtype">const unsigned int </td>
<td class="paramname"><em>ind</em>, </td>
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<td class="paramtype">const double </td>
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<p>constructor : generate a unique index </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">myPM</td><td>the physical model the atom belongs to </td></tr>
<tr><td class="paramname">ind</td><td>give the unique index </td></tr>
<tr><td class="paramname">pos</td><td>the initial position of the created atom (array of 3 double) </td></tr>
</table>
</dd>
</dl>
<p class="reference">References <a class="el" href="classStructure.html#a693e6b047fc6bb216b7646e0c2599070">Structure::properties</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a6926cfb6d5e61ca21c71476b66547a5e">◆ </a></span>~Atom()</h2>
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<td class="memname">Atom::~Atom </td>
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<p>std destructor </p>
<p class="reference">References <a class="el" href="classStructure.html#a693e6b047fc6bb216b7646e0c2599070">Structure::properties</a>.</p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a8408c7d4ed28ab1c0ef49035ccea4e86">◆ </a></span>getIndexInAtoms()</h2>
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<td class="memname">unsigned int Atom::getIndexInAtoms </td>
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<p>get the index of this atom in the global atom structural component, i.e. its order number in atoms </p>
<p class="reference">References <a class="el" href="classAtom.html#aba7e868fb492a66507780d8c9f4af6e7">indexInAtoms</a>.</p>
<p class="reference">Referenced by <a class="el" href="classPhysicalModel.html#a0082cd2e982102edaaac4d822f57d2e9">PhysicalModel::getPositionPointer()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a4ac7762cfcdfff37fe8cd4370a24d79b">◆ </a></span>getPosition()</h2>
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<td class="memname">void Atom::getPosition </td>
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<td class="paramtype">double </td>
<td class="paramname"><em>pos</em>[3]</td><td>)</td>
<td> const</td>
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<p>get the position of the atom (array of 3 doubles) </p>
<p class="reference">Referenced by <a class="el" href="classLoadsManager.html#a8df5657450299f799d8a04f5e6b22615">LoadsManager::addDecoration()</a>, <a class="el" href="classCreateSC.html#ab035f05c4872e8617367619a47e4966e">CreateSC::apply()</a>, <a class="el" href="classStructuralComponentDC.html#ab432ec381cef1a9687f6fad26a479fa2">StructuralComponentDC::atomsToGeometry()</a>, <a class="el" href="classMonitorNormDisplacement.html#abf06852951876d92b888966f8f90614e">MonitorNormDisplacement::calculate()</a>, <a class="el" href="classMonitorGeometricDeviation.html#a4c3560f8bc2959ea55498b7e422f892d">MonitorGeometricDeviation::calculate()</a>, <a class="el" href="classMonitorDistanceZ.html#a181692caa50ecef6379cf9dd6fa47b5f">MonitorDistanceZ::calculate()</a>, <a class="el" href="classMonitorPointSetDistance.html#aa24f9d5efe3ff0534e345e081fb82ff2">MonitorPointSetDistance::calculate()</a>, <a class="el" href="classMonitorPosition.html#ae8675e676e755ab2352041c3ba00b21c">MonitorPosition::calculate()</a>, <a class="el" href="classMonitorRen.html#a68e78cc8129f02a4a29f9f2c326800bf">MonitorRen::calculate()</a>, <a class="el" href="classMonitorDisplacement.html#a58f28e64894e7c776342dc8fdd1bf9c3">MonitorDisplacement::calculate()</a>, <a class="el" href="classMonitorDistanceY.html#aaaa0236ebf1a7af70757ac30169b7390">MonitorDistanceY::calculate()</a>, <a class="el" href="classMonitorPointToTriangleMeshDistanceFinal.html#aee938504ef7c8e7129f3b8516b591386">MonitorPointToTriangleMeshDistanceFinal::calculate()</a>, <a class="el" href="classMonitorDistanceX.html#a83d55f78b6b48fc63ec7efb140d6a94a">MonitorDistanceX::calculate()</a>, <a class="el" href="classMonitorPointFinalSetDistance.html#acd86091a40e97cf0108ee8e14194d3f8">MonitorPointFinalSetDistance::calculate()</a>, <a class="el" href="classPosition.html#ab6be1a6220734ca96dab7bfcad0e4029">Position::calculate()</a>, <a class="el" href="classCreateSC.html#aa587d1948bb2ce26a13968782f0a5c1d">CreateSC::computeBoundsOfPointIds()</a>, <a class="el" href="classPMLExplorerWidget.html#a9ef89f0994e42b298342500e8aef0f0e">PMLExplorerWidget::createAtomPropertyList()</a>, <a class="el" href="classPhysicalModel.html#aff8a12ee78a49eec540ebe21419e83fd">PhysicalModel::exportAnsysMesh()</a>, <a class="el" href="classPhysicalModel.html#a20029f79cf4097475ba6860432435d3d">PhysicalModel::exportPatran()</a>, <a class="el" href="classPMManagerDC.html#a2faf1ab5b2a540b4486059648da357de">PMManagerDC::getBounds()</a>, <a class="el" href="classReference.html#aa617c2c9b8f0a034fd8bdd944fe0b24e">Reference::getDistanceToTriangularMesh()</a>, <a class="el" href="classReference.html#aa15b22233ce91120d625c4b0fd5a5665">Reference::getNearest()</a>, <a class="el" href="classAtomDCProperties.html#aea82585bc2723d2cd5b6d225d59d280c">AtomDCProperties::getPosition()</a>, <a class="el" href="classAtomDC.html#a6e3befe018c4bb2d5824de2352bdc9d6">AtomDC::getPosition()</a>, <a class="el" href="classLoadsSimulationDriver.html#a12b248dada7c62507d1c656e14ef5504">LoadsSimulationDriver::init()</a>, <a class="el" href="classAtomDC.html#a89402d5de4c130197073b6066687481f">AtomDC::initRepresentation()</a>, <a class="el" href="classStructuralComponentDCPopup.html#a35261d16bb247044215a7f14426c1ae9">StructuralComponentDCPopup::saveToCsv()</a>, <a class="el" href="classSofaSimulator.html#a3dd7dfb188d8923b3c8577d2db19909b">SofaSimulator::SofaSimulator()</a>, <a class="el" href="classStructuralComponentDC.html#abe3087560e21ef1f5996664678bbb351">StructuralComponentDC::structuralComponentToVtk()</a>, <a class="el" href="classAnyDecoration.html#a33a4897c05e82cfd20d18c6410c3d5a2">AnyDecoration::update()</a>, <a class="el" href="classAtomDecoration.html#a2241aeb2ea5e289c2f3ad6d9efa4b6d0">AtomDecoration::update()</a>, <a class="el" href="classLoadsSimulationDriver.html#a53539260f2c07ae33ae1b297e603037e">LoadsSimulationDriver::updateAtomData()</a>, <a class="el" href="classAtomDC.html#acdefe586bfa2487f9a8630ee65dfd66f">AtomDC::updatePosition()</a>, <a class="el" href="classStructuralComponentDC.html#aaf8bc918719311f67c9b0c7c6675636d">StructuralComponentDC::updatePosition()</a>, and <a class="el" href="classLoadsSimulationDriver.html#adfbd98f9e0b8b5d95961bfb1f57c791c">LoadsSimulationDriver::updatePositions()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#acb191b6088ce3d936909d9f7c5fc8848">◆ </a></span>getProperties()</h2>
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<td class="memname"><a class="el" href="classAtomProperties.html">AtomProperties</a> * Atom::getProperties </td>
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<p>Get a ptr to the <a class="el" href="classAtomProperties.html" title="This class manages all the properties attached to an atom. ">AtomProperties</a>. </p>
<p class="reference">Referenced by <a class="el" href="classPMLExplorerWidget.html#a9ef89f0994e42b298342500e8aef0f0e">PMLExplorerWidget::createAtomPropertyList()</a>, <a class="el" href="classAtomDCProperties.html#ac8b2223dfcdf43985193ee97198ac586">AtomDCProperties::event()</a>, <a class="el" href="classPhysicalModel.html#a390622b07737de73554bdb0660e6b0d9">PhysicalModel::parseTree()</a>, <a class="el" href="classPhysicalModel.html#aefaeddf0b7e61ff35d91ac97de791b99">PhysicalModel::setAtoms()</a>, and <a class="el" href="classAtomDCProperties.html#ab16502e2c60d52c6baf0c440c43a8776">AtomDCProperties::updateProperties()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ae658592f948de366f4946af0c87370c3">◆ </a></span>isInstanceOf()</h2>
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<td class="memname">bool Atom::isInstanceOf </td>
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<p>return true only if the parameter is equal to "Atom" </p>
<p>Implements <a class="el" href="classStructure.html#a9582ed9349b39ebbc7db475421e6abd6">Structure</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aab8d61ef48ffe599b893391dd845db6d">◆ </a></span>setIndex()</h2>
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<td class="memname">bool Atom::setIndex </td>
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<p>set the index. </p>
<p>The index <b>have to be unique</b> otherwise this method has no effect. The sub-classes method will check that this index is not in use. </p><dl class="section return"><dt>Returns</dt><dd>true only if the index of the structure was changed </dd></dl>
<p>Reimplemented from <a class="el" href="classStructure.html#afd2e8e677876ca72829350653597b83b">Structure</a>.</p>
<p class="reference">References <a class="el" href="classPhysicalModel.html#a9815829e85b3322c81e3dadda6b1e892">PhysicalModel::addGlobalIndexAtomPair()</a>, <a class="el" href="classProperties.html#a316aad45126d00309435baa16037c524">Properties::getPhysicalModel()</a>, <a class="el" href="classStructure.html#a693e6b047fc6bb216b7646e0c2599070">Structure::properties</a>, and <a class="el" href="classStructure.html#afd2e8e677876ca72829350653597b83b">Structure::setIndex()</a>.</p>
<p class="reference">Referenced by <a class="el" href="classAtomDCProperties.html#a6779f6280b7ed00ea090c5819e973e20">AtomDCProperties::setIndex()</a>.</p>
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<td class="memname">void Atom::setPosition </td>
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<td class="paramtype">const double </td>
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<p>set the position of the atom </p>
<p class="reference">Referenced by <a class="el" href="classPhysicalModel.html#a9cf224cead2e202d9b72997a0e9344d3">PhysicalModel::setAtomPosition()</a>, <a class="el" href="classAtomDC.html#a92b082c8ccf6b88789d48fa7249cb348">AtomDC::setPosition()</a>, <a class="el" href="classSimulator.html#ab9b316501ec4e0fc8aea99239d23459a">Simulator::updatePositions()</a>, and <a class="el" href="classLoadsSimulationDriver.html#adfbd98f9e0b8b5d95961bfb1f57c791c">LoadsSimulationDriver::updatePositions()</a>.</p>
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<td class="memname">void Atom::setPosition </td>
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<p>set the position of the atom </p>
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<h2 class="memtitle"><span class="permalink"><a href="#a0a6980eff6c5753e153b97b75bb831dc">◆ </a></span>xmlPrint()</h2>
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<td class="memname">void Atom::xmlPrint </td>
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<td class="paramtype">const <a class="el" href="classStructuralComponent.html">StructuralComponent</a> * </td>
<td class="paramname"><em>sc</em> </td>
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<p>print to an output stream in "pseudo" XML format. </p>
<p>Implements <a class="el" href="classStructure.html#a480a6874d516d72c8d3632973665c39a">Structure</a>.</p>
<p class="reference">References <a class="el" href="classPhysicalModel.html#ae720fd27ed439db6026e8e437b51e22d">PhysicalModel::getAtoms()</a>, <a class="el" href="classStructure.html#a04b2fc52d7cc2af4356620f1d7e09c18">Structure::getIndex()</a>, <a class="el" href="classProperties.html#a316aad45126d00309435baa16037c524">Properties::getPhysicalModel()</a>, and <a class="el" href="classStructure.html#a693e6b047fc6bb216b7646e0c2599070">Structure::properties</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#aba7e868fb492a66507780d8c9f4af6e7">◆ </a></span>indexInAtoms</h2>
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<td class="memname">unsigned int Atom::indexInAtoms</td>
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<p class="reference">Referenced by <a class="el" href="classAtom.html#a28755c30bfc63e44babeaa264025c2b9">Atom()</a>, and <a class="el" href="classAtom.html#a8408c7d4ed28ab1c0ef49035ccea4e86">getIndexInAtoms()</a>.</p>
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<hr/>The documentation for this class was generated from the following files:<ul>
<li><a class="el" href="Atom_8h_source.html">Atom.h</a></li>
<li><a class="el" href="Atom_8cpp.html">Atom.cpp</a></li>
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